RNA-Seq: a revolutionary tool for transcriptomics
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TLDR
The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.Abstract:
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.read more
Citations
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Journal ArticleDOI
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li,Colin N. Dewey +1 more
TL;DR: It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal ArticleDOI
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas,Alexie Papanicolaou,Moran Yassour,Moran Yassour,Manfred Grabherr,Philip D. Blood,Joshua C. Bowden,M. B. Couger,David Eccles,Bo Li,Matthias Lieber,Matthew D. MacManes,Michael Ott,Joshua Orvis,Nathalie Pochet,Nathalie Pochet,Francesco Strozzi,Nathan T. Weeks,Rick Westerman,Thomas William,Colin N. Dewey,Robert Henschel,Richard D. LeDuc,Nir Friedman,Aviv Regev +24 more
TL;DR: This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
Journal ArticleDOI
A scaling normalization method for differential expression analysis of RNA-seq data
TL;DR: A simple and effective method for performing normalization is outlined and dramatically improved results for inferring differential expression in simulated and publicly available data sets are shown.
Journal ArticleDOI
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
TL;DR: GEPIA (Gene Expression Profiling Interactive Analysis) fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources.
References
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Journal ArticleDOI
Translational regulation of GCN4 and the general amino acid control of yeast.
TL;DR: M mammalian cells use the same strategy to downregulate protein synthesis while inducing transcriptional activators of stress-response genes under various stressful conditions, including amino acid starvation.
Journal ArticleDOI
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
Jill Cheng,Philipp Kapranov,Jorg Drenkow,Sujit Dike,Shane Brubaker,Sandeep Patel,Jeffrey Long,David Stern,Hari Tammana,Gregg Helt,Victor Sementchenko,Antonio Piccolboni,Stefan Bekiranov,Dione K. Bailey,Madhavan Ganesh,Srinka Ghosh,Ian Bell,Daniela S. Gerhard,Thomas R. Gingeras +18 more
TL;DR: The transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A– annotated transcripts and unannotated transcripts of unknown function, which has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.
Journal ArticleDOI
Stem cell transcriptome profiling via massive-scale mRNA sequencing.
Nicole Cloonan,Alistair R. R. Forrest,Alistair R. R. Forrest,Gabriel Kolle,Brooke Gardiner,Geoffrey J. Faulkner,Mellissa K Brown,Darrin Taylor,Anita L Steptoe,Shivangi Wani,Graeme Bethel,Alan J. Robertson,Andrew C. Perkins,Stephen J. Bruce,Clarence Lee,Swati Ranade,Heather E. Peckham,Jonathan M. Manning,Kevin McKernan,Sean M. Grimmond +19 more
TL;DR: A massive-scale RNA sequencing protocol, short quantitative random RNA libraries or SQRL, is developed, highlighting how SQRL can be used to characterize transcriptome content and dynamics in a quantitative and reproducible manner, and suggesting that the understanding of transcriptional complexity is far from complete.
Journal ArticleDOI
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
Paul Bertone,Viktor Stolc,Viktor Stolc,Thomas Royce,Joel Rozowsky,Alexander E. Urban,Xiaowei Zhu,John L. Rinn,Waraporn Tongprasit,Manoj P. Samanta,Sherman M. Weissman,Mark Gerstein,Michael Snyder +12 more
TL;DR: This work constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome and found 10,595 transcribed sequences not detected by other methods.
Journal ArticleDOI
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
Brian T. Wilhelm,Brian T. Wilhelm,Samuel Marguerat,Samuel Marguerat,Stephen Watt,Stephen Watt,Falk Schubert,Falk Schubert,Valerie Wood,Ian Goodhead,Ian Goodhead,Christopher J. Penkett,Christopher J. Penkett,Jane Rogers,Jürg Bähler,Jürg Bähler +15 more
TL;DR: High-throughput sequencing of complementary DNAs (RNA-Seq) and strand-specific array data provide rich condition-specific information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus improving the existing genome annotation.
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